A Hitchiker’s Guide to Open Science at ARNA

Section 1: What is Open Science and why should I care?

What is Open Science?

Movement to make scientific research, data, and dissemination accessible to all levels of society.

Key components:

  • Open Access: Free availability and unrestricted use of research articles.

  • Open Data: Sharing data freely for anyone to use, reuse, and redistribute.

  • Open Methodology: Transparency in research methods.

  • Open Source: Use and development of software, freely accessible and modifiable.

  • Open Peer Review: Transparent review processes to enhance research credibility.

  • Open Educational Resources: Free access to educational materials and resources

Why should I care?

  • Reproducibility: Facilitates the verification and replication of research results.

  • Increased Collaborations, across academia, industry, public authorities, citizen groups.

  • Accelerated Innovation: Faster progress through shared knowledge and resources

  • Greater Impact through wider dissemination

  • Enhanced Transparency: Promotes trust in scientific findings

  • Public Engagement, fostering a more scientifically literate society.

Why should I care? Examples

I can reuse and adapt this figure:

Understanding open science, 2022, UNESCO, doi: 10.54677/UTCD9302

Or I can re-use curated, high-quality data from a far-away university to make my own plots

#INSERT RACHAMANDRAN#

Why should I care?, but for pragmatists

  • Some aspects of it are made mandatory by funding agencies, trustees

  • Open Science practices are evaluated in funding/fellowship proposals

    • E.g. Criterion 1.2 of Criterion 1 (Excellence) of MSCA fellowship: Soundness of the proposed methodology (including […] the quality of open science practices)

But people will steal my stuff!

“As open as possible, as closed as necessary”: Results and data may be kept closed if making them public in open access is against the researcher’s legitimate interests, e.g.

  • commercially exploitation of research results

  • if it is against any obligations mentioned in the Grant Agreement (e.g. personal data protection)

Practically, what can I do?

  • Publish in Open Access journals

    • or make your preprint and/or accepter manuscript available

  • Share your data in open repositories

  • Use open-source tools and software

    • And make yours open

  • Advocate for Open Science policies in your institution

    • Please ARNA, pay for my APCs 🤑

  • Educate others about the importance and benefits of Open Science

Section 2: How to publish Open papers without having to sell a kidney

Archiving on a pre-print repository

  • Free and with good visibility for well-known repositories (BioRχiv, ChemRxiv)

    • Indexed in e.g. Google Scholar
    • Has a DOI, citable

  • Supported by many publishers

  • Possible to revise the manuscript and thus to upload accepted manuscript

  • Possible to link final paper to preprint

  • Authors retain copyright

  • Authors establish precedence

Example of BioRχiv deposition

Choose an open access modality

  • Self-archiving on repositories or personal sites

  • Uses pre-prints or post-prints (not final publisher version)

  • May have embargo periods

  • Free access; no APCs

  • Published in fully OA journals

  • Immediate access to final published version

  • APCs usually required

  • High visibility and wide dissemination

  • No APCs for authors or readers

  • Often funded by institutions, societies, governments

  • Focuses on providing free access to both readers and authors

  • Free and equitable access for all

  • Subscription journals with optional OA per article

  • Authors pay APCs for OA

  • Meets OA mandates

  • “Double-dipping”: subscriptions and APCs

INSERM’s opinion [source]

Certaines revues fonctionnent selon un modèle hybride : les articles y sont a priori publiés selon le modèle classique (payant pour le lecteur), mais la revue donne le choix aux auteurs de payer pour que leur travail soit publié en libre accès (payant pour l’auteur). Publier en Open Access dans ce type de revue est dès lors fortement déconseillé car cela entraîne un double paiement : celui de l’abonnement pour consulter l’ensemble de la revue et celui des frais de publication en Open Access

Choose a license [1/2]

The license impacts what people can do with your work, e.g.

  • CC BY: Reusers can distribute

    • if attribution given

    • remixed, adapted, built upon

    • including for commercial use

  • CC BY-NC-ND: Reusers can copy and distribute the work

    • if attribution given

    • in unadapted form only

    • for non-commercial use only

Choose a license [2/2]

The license impacts the article processing charges a.k.a APC

Archiving after publication

  • The go-to repository in France is HAL

    • Somewhat redundant local initiative @UBx: OSKAR

  • For PhD thesis: theses.fr

Disclaimers

  • Publishers may require the addition of disclaimers on top of accepted/published manuscript depositions

    • Publishers and public-mandate dependent, e.g. ACS

So when can I upload the publishers’ version exactly?

xxx

Section 3: Data, code and software

Go FAIR

  • F1. (Meta)data are assigned a globally unique and persistent identifier

  • F2. Data are described with rich metadata (defined by R1)

  • F3. Metadata clearly and explicitly include the identifier of the data they describe

  • F4. (Meta)data are registered or indexed in a searchable resource

  • A1. (Meta)data are retrievable by their identifier using a standardised communications protocol

    • A1.1 The protocol is open, free, and universally implementable

    • A1.2 The protocol allows for an authentication and authorisation procedure, where necessary

  • A2. Metadata are accessible, even when the data are no longer available

  • I1. (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.

  • I2. (Meta)data use vocabularies that follow FAIR principles

  • I3. (Meta)data include qualified references to other (meta)data

  • R1. (Meta)data are richly described with a plurality of accurate and relevant attributes

    • R1.1. (Meta)data are released with a clear and accessible data usage license

    • R1.2. (Meta)data are associated with detailed provenance

    • R1.3. (Meta)data meet domain-relevant community standards

Data management plan

Important service to generate your DMP, made mandatory by many funding agencies

  • DMP OPIDoR to plan your data management

  • Cat OPIDoR, a wiki of services dedicated to research data

  • PID OPIDoR for DOI.

    • Must request account creation to access DataCite

Learn more here.

Share data

Zenodo,…

Share software

GitHub, GitLab, BitBucket,…

Section 4: Resources

General resources

  • Research Ministry [FR]
  • Ouvrir la science! [FR/EN]
    • French Committee for Open Science
    • Ensures the implementation of the National Open Science Policy
    • Publishes guides, workshop reports
    • Publishes a small (and pretty) Encyclopedia of Open Science: https://encyclo.ouvrirlascience.fr/

Funding agencies and trustees

Specific resources: Publishing

  • Couperin consortium [FR]: Negociates on behalf of public entities for publication access/publishing costs (among other things)

  • Preprint repositories

  • Post-publishing repositories

    • HAL [FR/EN]: National repository

    • OSKAR [FR/EN]: UBx repository

  • Licensing

Specific resources: Data, code and software